Contacts of the helix formed by residues 159 - 171 (chain U) in PDB entry 6FF7
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 159 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109U TRP* 5.3 14.1 - - + -
156U SER* 3.1 16.5 + - - +
157U LEU 3.8 1.0 - - - +
158U GLU* 1.3 76.8 - - - +
160U ASP* 1.3 61.1 + - - +
161U LEU* 3.2 4.0 - - + +
162U ILE* 3.0 16.0 + - + +
163U ARG* 2.8 27.4 + - - +
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Residues in contact with ASP 160 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157U LEU 5.2 0.2 - - - -
158U GLU 3.5 5.6 + - - -
159U VAL* 1.3 70.9 - - - +
161U LEU* 1.3 58.2 + - - +
163U ARG* 3.8 6.9 - - - +
164U SER* 2.9 34.3 + - - -
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Residues in contact with LEU 161 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112U PHE* 5.4 10.3 - - + +
113U LYS* 5.4 8.3 - - + -
116U PRO* 5.2 15.3 - - + -
119U PHE* 5.7 10.0 - - + +
159U VAL* 3.2 4.4 - - + +
160U ASP* 1.3 80.1 - - - +
162U ILE* 1.3 60.9 + - - +
164U SER* 4.0 5.5 + - - -
165U GLN* 3.9 13.7 + - - +
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Residues in contact with ILE 162 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153U CYS* 4.7 17.7 - - + +
156U SER* 3.9 18.4 - - - +
157U LEU* 5.5 0.2 - - - -
159U VAL* 3.0 15.6 + - + +
161U LEU* 1.3 78.3 - - - +
163U ARG* 1.3 66.4 + - - +
164U SER 3.2 0.2 - - - -
165U GLN* 3.0 16.6 + - - +
166U VAL* 3.0 15.2 + - + +
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Residues in contact with ARG 163 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157U LEU* 3.3 34.9 + - + +
159U VAL 2.8 9.4 + - - +
160U ASP* 3.8 7.9 - - - +
162U ILE* 1.3 78.3 - - - +
164U SER* 1.3 56.6 + - - +
166U VAL* 4.4 5.6 - - - +
167U GLN* 2.9 33.4 + - - +
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Residues in contact with SER 164 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160U ASP 2.9 17.7 + - - -
161U LEU* 4.2 6.3 - - - -
162U ILE 3.2 0.4 - - - -
163U ARG* 1.3 76.1 - - - +
165U GLN* 1.3 57.8 + - - +
167U GLN* 4.5 9.7 - - - +
168U GLN* 5.3 1.4 + - - +
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Residues in contact with GLN 165 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120U PRO* 5.6 7.2 - - + -
123U PHE* 4.4 23.1 - - + -
161U LEU 3.9 8.8 + - - +
162U ILE* 3.0 11.2 + - - +
164U SER* 1.3 80.7 - - - +
166U VAL* 1.3 61.9 + - + +
167U GLN 3.4 0.6 + - - -
168U GLN* 4.1 11.6 + - - +
169U LEU* 4.7 2.9 + - - +
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Residues in contact with VAL 166 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153U CYS* 5.6 10.5 - - + +
154U PHE* 5.7 5.6 - - - -
157U LEU* 6.1 4.0 - - + -
162U ILE 3.0 15.2 + - - +
163U ARG* 3.1 6.0 + - - +
165U GLN* 1.3 74.2 - - - +
167U GLN* 1.3 66.0 + - - +
168U GLN 3.2 2.9 - - - -
169U LEU* 2.8 26.2 + - + +
170U ILE* 3.5 8.1 + - + +
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Residues in contact with GLN 167 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163U ARG 2.9 15.9 + - - +
164U SER* 4.6 9.2 - - - +
165U GLN 3.4 0.4 - - - -
166U VAL* 1.3 75.8 - - - +
168U GLN* 1.3 61.0 + - - +
169U LEU 3.2 0.5 + - - -
170U ILE* 3.2 3.8 + - - +
171U SER* 3.1 30.2 + - - -
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Residues in contact with GLN 168 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164U SER 5.3 0.4 + - - -
165U GLN 4.1 9.0 + - - +
166U VAL 3.2 0.8 - - - -
167U GLN* 1.3 79.4 - - - +
169U LEU* 1.3 59.5 + - - +
170U ILE 3.3 0.6 + - - -
171U SER* 4.5 5.8 + - - +
173U PRO* 5.6 2.8 - - - +
174U MET* 5.1 3.5 + - - +
215U ALA* 5.8 2.5 - - - +
218U GLU* 3.9 18.3 - - + +
219U ARG* 3.9 20.6 + - - +
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Residues in contact with LEU 169 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165U GLN 4.7 2.4 + - - +
166U VAL* 2.8 17.5 + - + +
168U GLN* 1.3 78.1 - - - +
170U ILE* 1.3 58.4 + - + +
171U SER 3.8 0.4 - - - -
174U MET* 3.9 14.6 - - - +
218U GLU* 3.7 19.0 - - + +
219U ARG 4.9 0.9 - - - +
221U PHE* 5.3 7.4 - - + -
222U LEU* 4.7 16.4 + - + +
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Residues in contact with ILE 170 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166U VAL* 3.5 8.3 + - + +
167U GLN* 3.2 4.4 + - - +
169U LEU* 1.3 82.7 - - + +
171U SER* 1.3 63.1 + - - +
174U MET* 4.7 2.2 - - - -
265U PRO 4.2 19.4 - - - +
266U THR* 4.5 18.9 - - - +
268U ARG* 5.8 0.3 - - - +
269U TRP* 3.9 14.7 + - - +
270U PHE* 5.1 7.2 + - + +
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Residues in contact with SER 171 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167U GLN* 3.1 15.9 + - - -
168U GLN* 4.5 5.4 + - - -
169U LEU 3.8 0.6 - - - -
170U ILE* 1.3 79.3 - - - +
172U LEU* 1.3 69.3 + - - +
173U PRO* 3.2 7.6 - - - -
174U MET* 2.9 21.0 + - - +
269U TRP* 4.1 6.1 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il